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Fig. 1 | Genetics Selection Evolution

Fig. 1

From: Muscle glycogen level and occurrence of acid meat in commercial hybrid pigs are regulated by two low-frequency causal variants with large effects and multiple common variants with small effects

Fig. 1

Pinpointing PRKAG3 R200Q as underlying a major QTL for residual glycogen level (RG) in muscle on SSC15. a A Manhattan plot of the initial GWAS for RG level with 60 K SNP data. The red and green dots represent the SNPs that reached genome-wide significance (P < 1.27e−6) and chromosome-wide significance level (P < 2.54e−5). b Regional association plot for RG level in the region between 114 and 124 Mb on SSC15 where 73 additional markers were incorporated. Two completely-linked and top SNPs were revealed: PRKAG3 R200Q and L53P (highlighted by red and orange dots, respectively), which were far more significant than the original top SNP rs326377357. The levels of linkage disequilibrium (LD) between the PRKAG3 R200Q and its surrounding SNPs are indicated by different colors. c Effects of nine haplotypes that include seven SNPs (T30N, G52S, L53P, 193A, 194L, I199V and R200Q) in PRKAG3 on RG level. Only the ninth haplotype that includes the 200Q and 53L alleles could cause a much higher RG level compared to the other eight haplotypes (P < 0.001)

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Genetics Selection Evolution

ISSN: 1297-9686